Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome
Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome
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DOI：
10.1016/j.jmb.2005.02.044
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发表时间：
2005-05-20
影响因子：
5.6
通讯作者：
Jeltsch, A
中科院分区：
文献类型：
--
作者：
Handa, V;Jeltsch, A
哺乳动物DNA甲基转移酶甲基化CG二核苷酸内的胞嘧啶残基。通过对人类表观基因组计划的已发表数据的统计分析，我们确定了中心CG位点周围最多+/-4个碱基对的侧翼序列，这些序列是人类基因组DNA中高（5 '-CTTGCGCAAG-3'）和低（5 '-TGTTCGGTGG-3'）甲基化水平的特征。我们已经研究了侧翼序列对Dnmt 3a和Dnmt 3b从头DNA甲基转移酶的催化活性的影响，使用一组合成的寡核苷酸底物，其在定量方面覆盖所有可能的+/-1侧翼。甲基化动力学实验揭示了优选的（RCGY）和不利的+/-1侧翼碱基对（YCGR）之间> 13倍的差异。此外，富含AT的侧翼优于富含GC的侧翼。这些实验偏好与基因组甲基化模式一致。因此，我们扩展了我们的实验分析，发现基因组中高水平和低水平甲基化的共有序列的甲基化率差异> 500倍。该结果证明了Dnmt 3a和Dnmt 3b的非常明显的侧翼序列偏好。这表明，人类DNA的甲基化模式是由于，部分地，从头DNA MTases的侧翼序列的偏好和侧翼序列的偏好可能参与CG岛的起源。此外，已经发现类似的侧翼序列偏好用于通过未甲基化的CG刺激免疫系统，这表明DNA MTases和免疫系统的共进化。(c)2005爱思唯尔有限公司保留所有权利。
Mammalian DNA methyltransferases methylate cytosine residues within CG dinucleotides. By statistical analysis of published data of the Human Epigenome Project we have determined flanking sequences of up to +/- four base-pairs surrounding the central CG site that are characteristic of high (5'-CTTGCGCAAG-3') and low (5'-TGTTCGGTGG-3') levels of methylation in human genomic DNA. We have investigated the influence of flanking sequence on the catalytic activity of the Dnmt3a and Dnmt3b de novo DNA methyltransferases using a set of synthetic oligonucleotide substrates that covers all possible +/- 1 flanks in quantitative terms. Methylation kinetics experiments revealed a > 13-fold difference between the preferred (RCGY) and disfavored +/- 1 flanking base-pairs (YCGR). In addition, AT-rich flanks are preferred over GC-rich ones. These experimental preferences coincide with the genomic methylation patterns. Therefore, we have expanded our experimental analysis and found a > 500-fold difference in the methylation rates of the consensus sequences for high and low levels of methylation in the genome. This result demonstrates a very pronounced flanking sequence preference of Dnmt3a and Dnmt3b. It suggests that the methylation pattern of human DNA is due, in part, to the flanking sequence preferences of the de novo DNA MTases and that flanking sequence preferences could be involved in the origin of CG islands. Furthermore, similar flanking sequence preferences have been found for the stimulation of the immune system by unmethylated CGs, suggesting a co-evolution of DNA MTases and the immune system. (c) 2005 Elsevier Ltd. All rights reserved.